Yale University
Department of Computer Science

GRADUATE HANDBOOK

2009-2010 Edition

1. Introduction

2. Research in Computer Science

3. Graduate Programs
3.1 The Doctoral Program
3.1.1. A Brief Overview of the Doctoral Program
3.1.2. Requirements
3.1.3. Evaluation of Progress
3.1.4. Miscellany
3.1.5. The Fast Track
3.1.6. Master’s Degrees en Route to the Ph.D.
3.2 The Master's Program

4. Departmental Computing Facilities

5. Graduate Student Life
5.1 The McDougal Graduate Student Center
5.1.1. Mission
5.1.2. Facilities
5.1.3. Student Life Programs
5.1.4. Graduate Career Services (GCS)
5.1.5. Office of Teacher Preparation
5.2 Life in the Department
5.3 Life About Town

6. Graduate Admissions and Financial Aid
6.1 Admissions Procedures
6.2 Financial Aid Policy

7. Graduate Courses

8. Personnel
8.1 Advanced Students
8.2 Recent Graduates

9. Graduate School Calendar

1. Introduction

The Yale Department of Computer Science was founded in 1969 as a small Ph.D. program. It now includes 21 regular faculty members, and more than 50 graduate students, including a thriving population of Master's-degree students.

The Ph.D. degree program in computer science stresses original research. To this end, the course requirements are minimal and students normally begin research by the fall term of their second year of graduate study. The terminal M.S. degree program in computer science brings students to the cutting edge of the field and provides them with a solid foundation on which to build their future careers.

In 2001, Yale celebrated its 300th anniversary. The Department of Computer Science is almost an order of magnitude younger, reaching its 32nd birthday in the same year. But its influence on the university, within the research community, and on society as a whole, belies its young age. Computers are a dominant presence in almost every walk of life, and it is becoming increasingly difficult for people to answer the question, “How did we ever live without them?”

The Department of Computer Science was founded by people who had a vision. This vision was how computer science would fit into the unique spirit of Yale University, an institution oriented to an unusual degree around undergraduate education and close interdepartmental collaboration. The Department has always had close ties to mathematics and engineering, but has increasingly experienced collaborations with other disciplines important to Yale, including art, architecture, biology, psychology, economics, business, statistics, linguistics, music, medicine, physics and more.

2. Research in Computer Science

An academic research effort in any field is supposed to establish outer boundaries. Commercial efforts demonstrate what is profitable; academic efforts show what is possible. In physics, mathematics and the other large, long-established areas, most research gains lead to relatively small changes in the character and perimeter of the field. Computer science is different. It’s brand new. When a few researchers parachuted into this field in the 1940’s, they had no territory to extend. They invented computer science from scratch, more or less. They faced basic questions in science, algorithms, design, and philosophy; and by answering them, they established the intellectual basis of the field. What does “computable” mean? How do we classify computations, distinguish practical from impractical from impossible? How should programming languages be designed, and what difference do they make? Is it possible in principle to build a mind out of software? And so on.

When the Department of Computer Science was founded in 1969, the fledgling field was viewed as consisting of four primary areas: theory of computation, artificial intelligence, numerical analysis, and systems. Over the years, these areas have developed so quickly in both depth and breadth that each now consists of many sub-areas. Within artificial intelligence, areas such as machine learning, knowledge acquisition systems, robotics, computer vision, neural networks, and more have grown. Systems research now includes graphics, databases, operating systems, networking, and the entire sub-field of programming languages, which includes formal semantics, compilers, programming environments, software engineering, and object-oriented, functional, and logic programming. Similarly, theory of computation now includes computability, complexity theory, design and analysis of algorithms, cryptography, distributed computing, discrete mathematics, and more. Each of these many new areas now boast their own conferences, journals, federal research programs, and so on.

Each of these areas also has developed into both theoretical and experimental disciplines. For example, security theory establishes the correctness and robustness of idealized cryptographic protocols, but real systems need to be built and fielded to ensure that the protocols withstand realistic attacks. Type theory and category theory help establish the foundations of programming languages, but real languages need to be designed and built to ensure that programmers can use them productively. And learning and planning theory tells us what the limits of automated intelligence are, but robots need to be built to demonstrate the viability of these results. At Yale, both theoretical research and applied research are valued highly.

Computer science has also grown beyond its own bounds to become a multi-disciplinary field that touches many other sciences as well as arts and humanities. Aside from the obvious overlaps with engineering and mathematics, there are natural connections with physics, economics, law, management, psychology, biology, medicine, music, philosophy, and linguistics. Indeed, members of the computer science faculty have engaged in collaborations with each of these areas. These efforts have affected our curriculum through the establishment of cross-listed courses, interdisciplinary majors (such as cognitive science), special “tracks” and dual majors, and the creation of the Applied Math program. They have also led to interdisciplinary research centers, such as the Center for Scientific Computing (CS, Math), the Center for Computational Vision and Control (CS, EE, and Medicine) and the Center for Internet Studies (CS, SOM, and Law). Most recently, the C2 Initiative (Creative Consilience of Computing and the Arts) provides students with opportunities to apply mathematical, computational, and technological tools to problems inspired by the arts (Art, Art History, Music, Theater Studies, and Architecture).


Of course, with such diversity and depth, it has become increasingly difficult for any Department of Computer Science to cover all areas, and no one really tries. The many changes that are taking place in the field have led the Department to pursue a vision for the future a bit different from the original structure upon which it was founded. At Yale, the current focus of computer science is in these specific areas: algorithms and complexity theory, databases, distributed computing, machine learning, programming languages and compilers, scientific computing and applied math, graphics, vision and robotics, and security and cryptography, and Computing and the Arts.

3. Graduate Programs

The Department offers two graduate programs: a doctoral program leading to a Doctor of Philosophy (Ph.D.) degree, and a terminal master’s program leading to a Master of Science (M.S.) degree. The doctoral program is intended for students preparing for a career in teaching and/or research. The terminal Master’s degree program is intended for students who want advanced study in computer science but do not intend to go on for the Ph.D.

A student may apply to either the doctoral program or to the terminal master’s program. A student seeking the Ph.D. should apply directly to the doctoral program, even though he or she intends to obtain a Master’s degree along the way. A student who has completed the Master’s program and decides to go on for a Ph.D. is not guaranteed admission to the doctoral program and must apply in the normal way.

3.1 The Doctoral Program

The Doctoral Program of graduate study leads to the Ph.D. degree and is normally completed in 4-5 years. The M.S. and the M.Phil degrees are granted to qualified students in the Ph.D. program who wish intermediate degrees. (See 3.1.6.)

3.1.1. A Brief Overview of the Doctoral Program

Here is how a Ph.D. student's career goes.

In the first year, the student is expected to take courses and familiarize himself or herself with the activities of the various research groups in the Department. By the end of the year, the student must have teamed up with a research advisor, a faculty member who takes primary responsibility for the student's progress. Hence every student should be engaged in negotiations with professors they might want to work with starting well before the end of the second term in order to identify a faculty advisor.

After the first year, the student comes under the direction of a supervisory committee, consisting of the advisor and two or three other faculty members who monitor and mentor the student. Usually the committee forms “automatically” and consists of faculty working in the same area as the advisor, but there are many exceptions, especially when the student's work crosses disciplinary or departmental boundaries. In particular, if the day-to-day advisor's primary appointment is not in the Department of Computer Science, the committee must have an “advisor of record” in the Department.

Once a student has selected a supervisory committee, any changes to the committee require consultation among the director of graduate studies, the old committee, and the proposed new one, and often require the approval of the entire faculty.

In the second year, the student continues taking courses, completing a total of ten courses by the end of the year. Two of these must be the CS-690 and CS-691 sequence, which are just a convenient rubric for the student's research project.
Each student must serve as a teaching assistant (TA) for two terms as a key part of academic training. First-year students are not normally eligible as TAs, so this requirement becomes relevant in the second year. However, it is not necessary to satisfy the teaching requirement entirely in that year.

The end of the second year is the culmination of two years of study and research. The student passes an area exam demonstrating breadth of knowledge in the research area of the 690 project, and finishes the 690 project itself, presenting the results to the faculty as a written “690 report.”

By the start of the third year, the student begins dissertation research, usually under the direction of the same supervisory committee. However, if the student or the committee believes that the research is not going well, this is a good time to pick a new advisor and research topic.

By the end of the third year, the student should have satisfied all requirements for admission to candidacy, including writing a thesis prospectus that describes the general area and direction of the dissertation research. The student is then admitted to candidacy by vote of the faculty. The Graduate School will not allow a student to register for a fourth year of study until this step has been completed.

After admission to candidacy, the student’s position in the Department is secure, subject only to continued satisfactory progress toward completion of the dissertation. When the dissertation is complete, it is defended before the faculty and approved by a committee of readers. It is turned into the Graduate School and the readers file reports approving it. The faculty then vote to recommend that a degree be granted based on the reader reports. The requirements for the Ph.D. have then been met and the degree is granted.

3.1.2. Requirements

The milestones along the way to the Ph.D. are described in detail below. The course requirements, examinations, and 690 project should be completed by the end of the second year, and all requirements for admission to candidacy must be completed by the end of the third year.

The dissertation and defense must be completed no later than the end of the sixth year. Exceptions to these rules require approval of the director of graduate studies, the faculty, and/or the Graduate School.

Course Requirements: Students are required to pass ten courses, satisfying the following constraints:

Two of the courses must be CS-690 and CS-691, independent project. These courses introduce the student to research. Grade requirement: CS-690 must be passed with a grade of SAT and CS-691 must be passed with a grade of HIGH PASS or HONORS. Two of the remaining courses must be passed with a grade of HONORS; the rest must be passed with a grade of at least HIGH PASS. Depth requirement: by the end of the second year, each student must pass three advanced courses in a particular field.

The following rules govern which courses may be counted towards the course requirements:

General constraints:

No course with number 499 or below can be used to satisfy a course requirement. Any 500-level course can be used to satisfy the 10-course requirement and the depth requirement. For example, if a theory student takes a 500-level theory course, it simultaneously counts toward both requirements.

The CS-690 and CS-691 course sequence counts only toward the 10-course and research requirements.

A 600-, 700-, or 800-level course can count towards the 10-course and depth requirements, but only if it involves regular meetings with a faculty member and tangible written work that can be evaluated, and results in a regular grade of HONORS or HIGH PASS. In practice, some but not all 600-level courses will count, while 700- and 800-level courses normally will not count towards any requirements.

Non-CS Department courses: A student can count a graduate-level course outside the Department towards the 10-course and depth requirements if it is relevant to the student’s program of study. This determination is made by the director of graduate studies, possibly in consultation with the student’s advisor.

Distribution constraints:

In these constraints, we use a pattern notation to indicate course classes. Every course has a three-digit number, Kdn. K must be greater than or equal to 5 (see above); n is arbitrary; the digit d is the most reliable indicator of the subject area of the course.

Two of the six courses must be in theoretical computer science, whose numbers typically have d=6. Currently they include CS-557, CS-560, CS-561, CS562, CS563, CS-565, CS-567, CS568 and CS-569. Two are in programming languages and systems, whose numbers typically have d = 2 or 3. One of these courses must be "programming intensive," requiring participation in a multi-person project whose goal is produce several thousand lines of code. The programming-intensive courses currently are CS-521, CS-522, and CS-537. Other courses in this category are CS533, CS538, and CS-534.

Two are in “applications,” typically having numbers with d = 4, 5, or 7. The list currently contains CS-540, CS-545, CS-570, CS-573, CS-575, CS-577, CS-578, CS-579, and CS-752.


The actual courses being offered tend to change faster than we can keep this list accurate and complete, so don't hesitate to check if you think a course should be classified differently from what the rules imply.

Other constraints:

All the courses should contain substantial material beyond what the student has learned before coming to Yale. If a student is unable to find courses satisfying the requirements above, the DGS will usually accept courses from other departments that are in similar topic areas. Seminars may be acceptable, too. These are courses presented on an ad-hoc basis and that may consist mainly of paper presentation and discussion. (Their numbers usually have d=7.) The DGS will approve such a course to satisfy the distribution requirement if a student has already studied deeply in a research area, and is strongly motivated to explore it further.

Official Graduate Student Talks In order to keep the faculty apprised of research progress, each student must give a public talk on the progress of his or her research twice during his career, once after completing a 690 project, and once after filing a dissertation prospectus. These talks are known as official graduate student talks (OGSTs). They are open to the public, and all members of the Department are welcome. OGSTs are good opportunities to practice giving talks, and, for incoming students, to learn how to give a talk — and what can go wrong! They are scheduled in the fall by the Department student coordinator on a first-come-first-served basis.

The student must announce the talk at least a week in advance on the appropriate e-mail lists (currently grad-students@cs.yale.edu and faculty-cs@cs.yale.edu). The announcement should be repeated as the date draws near. All OGST announcements should indicate the student’s year of study and the current 690 project advisor or thesis advisor. Students who have been admitted to candidacy should also list their reading committee and expected date of completion.

690 Project The student must submit a written report on his or her 690 project to his or her supervisory committee, which grades it for (a) quality of the work, (b) quality of the technical writing, and (c) quality of the English. The grade and a one-page abstract must be transmitted to the director of graduate studies.

Please note that the course grades for CS-690 and CS-691 are not the same as the grade for the 690 report. The advisor files a grade of “SAT” or “UNSAT” for CS-690 and HONORS or HIGH PASS for CS-691, indicating whether the student is making satisfactory progress toward completing the research and the report. If not, the supervisory committee and faculty should be notified. The course grade is submitted at the end of the term, with other course grades. The grade on the 690 report is submitted after the supervisory committee has read it and agreed on a grade, which may occur before or after the course grade is submitted.

Area Examination The student must pass an Area Examination by the end of the second year. The purpose of the area exam is to demonstrate proficiency in scholarship over a subject area that includes the area of the 690 project, but is broader. The exam is formulated and administered by the student’s supervisory committee. The committee will decide whether the same exam should be given simultaneously to a cohort of students, as opposed to giving each student his or her own exam.

The exam typically includes something like the following: A written or oral test of in-depth knowledge of the research area test of the capacity to learn a topic from research literature (e.g., an extended oral presentation and critique of one or more research papers); presentation of the 690 report and fielding of questions about it. This in-depth examination by the supervisory committee is not the same as the OGST, which is required of every student after acceptance of the 690 report, and is aimed at a more general audience.

Thesis Advisor A regular faculty member must agree to direct the student’s dissertation, thereby certifying that the student is capable of doing original research. Meeting this requirement does not automatically follow from the student’s receiving a grade of HONORS or HIGH PASS on the 690 project. The advisor may be a ladder faculty member from another Yale department, if the student’s supervisory committee and the DGS approve. It is generally unproductive for a student to attempt a dissertation in an area not covered by the faculty’s interests; faculty members will normally require a student to work in areas they care about. The thesis advisor must be chosen by the beginning of the third year.

Thesis Prospectus A thesis prospectus must be filed with the director of graduate studies and the Graduate School by the end of the 3rd academic year, this being a written summary (about 3 or 4 pages long) of the nature and scope of the thesis research and a tentative title of the dissertation. The prospectus must also include a proposed committee of readers (see below) and be signed by the advisor.

Admission to Candidacy The faculty will vote to admit the student to candidacy when all of the requirements described above have been satisfied: course requirements, 690 Project and Report, first OGST, area examination, thesis advisor, and a thesis prospectus. It is required that a student will be admitted to candidacy by the end of the third year. Because the prospectus is usually the last piece to fall into place, the prospectus must be done by then so that the department faculty can certify the student. If the requirements have not been satisfied by the beginning of the fourth year, the Graduate School will not allow the student to register for classes or to be paid, as a research assistant or teaching fellow. Undoing the damage requires negotiations with the Computer Science Department that usually result in the student being placed on probation for a term, assuming he or she is finally admitted to candidacy before the end of that tern. This language should not be taken as implying that the “real” deadline is August 31. Rather the end of the academic year is considered to be May.

The Dissertation The most important part of the Ph.D. program is research training, culminating in the writing of a dissertation. The dissertation should be concluded no later than the end of the student’s sixth year. The dissertation demonstrates the student’s ability to perform original research. Thus, it must demonstrate technical mastery of the subject and must contain conclusions that modify or enlarge what has previously been known. Because Yale is a university, dedicated to the dissemination of knowledge, all results of research, including the dissertation, must be made public. Access may not be restricted for any reason, commercial or governmental.

Thesis Defense The student must give an oral defense of the thesis research when the student’s committee is satisfied that the work is complete and the student has a complete draft of the dissertation ready to submit to the Graduate School. To ensure the latter, one copy of the dissertation must be given to the departmental registrar and made available to the Department faculty at least one week before the defense takes place. The dissertation must also be placed on the Department's web site on the “Internal/Faculty Use” page or in some more publicly accessible place.

The defense consists of a one-hour public presentation of the results followed by a 15-minute question and discussion period, which is open to the entire department and its guests. The faculty and outside readers then conduct an oral examination in closed session.

At least three readers must be present at the defense, although as technology improves virtual presence becomes more of a possibility. It is not necessary for the external reader to attend if plenty of internal ones are available.

In order to give all interested faculty the opportunity to attend, the defense must be scheduled with the director of graduate studies and announced to the faculty at least one month in advance. Thesis defenses are normally held at 3:45 on Wednesdays. An arrangement to hold one at another time must be made in agreement with the computer science faculty, as coordinated by the DGS.

Dissertation Submission The dissertation should be submitted to the Graduate School as soon as the thesis defense has been passed and any final corrections to the dissertation have been made. This must be completed within one month of passing the defense, or the student must defend again. A copy of the final draft must also be given to the departmental registrar. After the dissertation is submitted, copies are sent to the members of the reading committee (see below), who each read the thesis and complete a “reader’s report” form. When all reader reports are in, they are made available to the faculty, who then meet and vote whether to recommend the degree. The recommendation is forwarded along with the reader reports to the Graduate School, which reviews the recommendation. Finally, the entire graduate faculty votes to approve the degree.

In order to allow time for these steps to be completed in a timely fashion, the Graduate School requires that the dissertation be submitted by October 1 for a December degree and by March 15 for a May degree. These deadlines are strictly enforced.

Dissertation Readers The dissertation must be read by a committee of four readers, which is a distinct entity from the supervisory committee (although it normally overlaps with it). Three readers must be internal and one must be external. An internal reader may be any faculty-level person with a close affiliation to the Yale Department of Computer Science, including regular faculty, visiting faculty, research scientists, and associate research scientists. An external reader may be any qualified person who is not closely affiliated with the Computer Science Department. In addition, the reading committee must conform to the following rules:

• At least two Internal Readers must be regular ladder faculty in the Yale Department of Computer Science;
• All Internal Readers are normally expected to attend the student’s OGST's and the Thesis Defense;
• At least three Readers must attend the Thesis Defense.

Exceptions to these rules require approval of the Director of Graduate Studies.

For the purposes of these regulations, “close affiliation” status is conferred by any extended visit in the Department or any kind of departmental appointment or title, including affiliate and adjunct titles. Occasional short-term visits or research collaborations do not constitute close affiliation. Once conferred, the status of “close affiliation” persists for a period of two years after the affiliation terminates. Thus, a faculty member who takes a position elsewhere may continue to serve as an internal reader for two years after leaving and may not serve as an external reader during that same period. The above notwithstanding, the reading committee must always include at least one current regular ladder faculty member in the Yale Department of Computer Science. In addition, if the advisor leaves Yale, the Graduate School may require that a current Yale faculty member serve as acting advisor.

The rules concerning the composition of the reading committee must be satisfied when the committee is first formed, at the time of the thesis defense, and at any time that the committee is changed.

3.1.3 Evaluation of Progress

Students must maintain a satisfactory rate of progress toward the Ph.D. in order to remain in good standing in the program. During the first year, progress is measured by formal course work. To remain in good standing, at least six courses must be completed with a grade of HIGH PASS or better.

After the first year, rate of progress is monitored by the student’s supervisory committee. The committee looks at grade records, exam results, the 690 report, and research progress. The committee is also expected to attend the student’s required OGST’s in order to see first-hand how the student is doing. Students beyond the first year receive written annual evaluations of their progress, drafted by the supervisory committee. A copy of this evaluation is placed in the student’s file. A decision that the student is not making satisfactory progress toward the Ph.D. may be made at any time by the supervisory committee.

Whenever a student is determined not to be in good standing, either by failing to achieve required milestones or by recommendation of his or her supervisory committee, the student and the faculty will be notified. All information regarding the student, including course grades, research performance, and performance on exams, will be made available to the faculty as a whole, which will then determine a course of action for the student. Possibilities at this stage can include continuation in the program with revised expectations, academic probation, or dismissal from the graduate program. The director of graduate studies will inform the student in writing of the faculty’s determination and, in case continuation in the program is permitted, of conditions that must be fulfilled to return or remain in good standing.

In cases where the sole reason for the student’s trouble is apparent inability to do research under the supervision of his or her current committee, the usual expectation is that a new committee will be formed and will give him or her an appropriate period of time (a term or a summer) to demonstrate ability to conduct a research project successfully. The committee will report to the faculty at the end of this period, so that a new decision can be made.

If the committee determines that the student has not yet passed one of the designated requirements, then the committee should report at that time, and as necessary in subsequent terms, on how the student is progressing towards satisfying the requirements, and what its recommendation is. The recommendation can range from “the student should be terminated” to “the student has satisfied all the requirements for admission to candidacy.” One possible recommendation is that the student change research area, under the direction of a new supervisory committee. This recommendation is not routine, and should not be considered the normal consequence of failing an area exam.

The supervisory committee’s evaluation is particularly crucial at the end of the second year, when the results of the 690 project and area exam become available. At this time, the supervisory committee is expected to report in writing to the faculty as a whole (as well as to the student) on the student’s status. This notification should be given by the middle of May, and a special faculty meeting will be held toward the end of May to act on any recommendations.

3.1.4. Miscellany

In order to gain teaching experience, all graduate students are required to serve as a teaching assistant for two terms during their first three years of study. Teaching performed in order to meet the obligations of financial aid packages can also be used to satisfy this requirement. Students who perform teaching not required by a financial aid package may receive additional compensation. (See 6.2)

The Graduate School requires that a Ph.D. student spends a minimum of three years in residence and that full tuition be paid for four years. If the student graduates in fewer than four years, with no leaves of absence, then any additional tuition is waived. Whether a student is in good standing is independent of whether there are funds to support him or her.

If a student’s advisor leaves Yale, then what happens depends on the student’s state of progress toward a Ph.D. A student who has not completed the three-year residency requirement and been admitted to candidacy will normally be expected to find a new advisor or go with the departing faculty member and enroll in another Ph.D. program. An advanced student normally finishes his or her dissertation while continuing under the technical supervision of the departed advisor and receives a Yale degree. In this case, the Graduate School may require that a current Yale faculty member agree to act as official advisor. Such a student will have two years to finish his or her dissertation before the Department will no longer be bound to accept it. The thesis defense must still be held at Yale, according to the usual rules.

Students can expect to have office space in Arthur K. Watson Hall, subject to availability, for their first six years.

3.1.5. The Fast Track

Fast-track status enables students whose computer science education is already well under way when they enter the Ph.D. program (e.g., after receiving a Master’s degree in CS from another institution) to take fewer courses and to get started sooner on research. A student who wants to get onto the fast track must discuss the issue with the DGS upon admission to the program. The status becomes official if, by the end of the first year of study, the student has taken CS690 (i.e., found an advisor and begun research) and passed six courses with grades of HIGH PASS or HONORS. The DGS will examine the student’s academic history to decide which courses already taken satisfy which distribution requirements, and which requirements remain to be satisfied. Students who expect to qualify as “fast track” may, with permission of the director of graduate studies, begin the 690 project in the first or second term of study. It may also be granted in those cases where the intended area examination covers work done for the 690 project (which is now the case in programming languages and systems). Such an early start on research will not affect the eventual attainment of fast-track status nor the number of courses that will be waived, both of which are determined as described above.

Here in detail is the procedure that is now required to certify that a student is taking the fast track: A table must be prepared showing which Yale courses are obviated by which graduate-numbered courses at the institution where the student earned their M.S. All of these courses must have been taken during the student’s post-graduate education, after the award of the Bachelor’s degree or equivalent. A theory course here must be paired with a theory course there, and so forth. However, the titles of the two courses do not have to be identical, or even similar, provided that in the judgment of the DGS the two courses occupy the same "ecological niche." That is, if Yale offered a course on that topic, it would be classified as a course that satisfied the same clause of the distribution requirement as the Yale course it is paired with. (Example: Suppose Yale offers a course on distributed sensor networks and the M.S. institution offers a course on mobile computing. These can be paired, because if Yale had a course on mobile computing it would satisfy the systems requirement.)

The DGS prepares a certificate incorporating this table and sends it to the Dean of the Graduate School, who must approve waiving the courses proposed by the Department of Computer Science. No more than three courses may be waived.

3.1.6. Master’s Degrees en Route to the Ph.D.

A student in the Doctoral Program can earn a Master of Science (M.S.) degree and/or a Master of Philosophy (M.Phil.) degree en route to the Ph.D. The requirements for the M.S. degree are described in 3.2 below. The requirements for the Master of Philosophy (M.Phil.) degree are the same as for the Ph.D. except for requirements having to do with the dissertation. Why anyone would want two Master's degrees is a mystery, but many students do.

3.2 The Master’s Program

The terminal Master’s Program of graduate study is normally completed in one year, but may be spread over as long as four years. To qualify for the Master of Science degree, the student must pass eight courses at the 500-level or above. These must satisfy the same "general constraints" as for Ph.D. students (see section 3.1.2.). An average grade of at least HIGH PASS is required, with at least one grade of HONORS.

A one-term Independent Project course (CS-690) may be applied towards the Master’s degree with prior permission of the Director of Graduate Studies, provided that a faculty member is willing to supervise the project, applying the same standards as for a Ph.D. student. The faculty is under no obligation to supervise independent projects for Master’s students.

Advanced graduate courses in other departments that involve concepts from computer science and are particularly relevant to an individual program may, with permission of the Director of Graduate Studies, be counted towards the degree. Generally at most two such courses may be used to satisfy the requirements of the Master’s Program. Here an advanced course is generally one with at least one intermediate course as a prerequisite and an intermediate course is generally one with at least one (introductory) course as a prerequisite. But five courses must be in computer science.

4. Departmental Computing Facilities

The faculty, researchers, and students in the Department of Computer Science have access to a wide variety of ever-changing state-of-the-art computing resources, ranging from laptops, conventional PC’s and scientific workstations to high-powered compute-servers and workstation clusters used as parallel computers.

All of the computer systems are interconnected by a switched Ethernet local network, which is connected to the Internet via fiber optic technology to the campus backbone. Also recently installed is a wireless network permitting instant laptop access to the Internet anywhere in the building and many places on campus.

Most faculty, Ph.D. students, and researchers are equipped with a personal workstation or advanced-technology PC, all running some variant of the Linux or Windows operating systems. The computing needs of undergraduate and master’s students are met through the "Zoo", an educational laboratory with approximately 40 dual-processor Linux workstations which allow for remote as well as on-site access.

Individual research groups have additional specialized equipment for robotics, computer vision, computer music, networking, and other research efforts. Students in computer science, both graduate and undergraduate, have liberal access to all of these facilities. In this way students play a vital role in contributing to our understanding of theoretical and experimental issues in computer science. The Department’s computing resources are professionally managed by Workstation Support Services (WSS), a unit of the Yale office of Information and Technology Services (ITS). WSS staff follow the policy set by a faculty oversight committee in providing first-class responsive service to all departmental users.

5. Graduate Student Life

5.1 The McDougal Graduate Student Center

Much of the graduate student life is based in the various departments and in dormitories or apartment complexes. The new McDougal Center is a place where graduate students from across the campus regularly meet and share interests. It is located in the Hall of Graduate Studies (HGS), 320 York Street (432-2583), mcdougal.center@yale.edu, http://www.yale.edu/mcdougal.

5.1.1 Mission

A generous gift from Mr. Alfred McDougal, a Yale alumnus, and his wife, Ms. Nancy Lauter, enabled Yale to create the McDougal Graduate Student Center in 1997. The McDougal Center provides space and program funding for building intellectual, cultural, and social life, and for facilitating professional development activities across the departments of the Graduate School of Arts and Sciences. The McDougal Center warmly welcomes the participation of students from other Yale Graduate and Professional Schools, postdoctoral fellows, faculty, staff, alumni/ of the Graduate School, and members of the larger Yale community. Its website (http://www.yale.edu/mcdougal) provides all kinds of information relating to graduate student life. The Center provides members of the graduate student community with a place of their own on campus.

5.1.2 Facilities

The facilities of the McDougal Center enhance student life in many ways. The magnificently restored Common Room has been transformed into a lounge with comfortable furnishings, internet ports, newspapers and magazines, and a student- run café serving coffee and light food throughout the day. In an adjacent wing on the first floor of HGS the Center has a large multi-purpose Program Room (HGS 119) with a portable stage, seating for up to 100, and advanced video and sound projection equipment. The Program Room provides space for lectures, conferences, performances, film series, workshops and other events by and for students. The Center also has smaller conference and meeting rooms. Graduate student groups and departments may request to reserve space by contacting the center office at 432-8273, stopping by HGS 123, or filling out a request online at www.yale.edu/mcdougal/facilities. There is a public computer cluster supported by Academic Computing Services, a public copy machine, a public phone, bulletin boards and information kiosks as well. The lower floor also offers offices for the Assembly of Graduate Students, graduate student organizations, rooms for Teaching Fellows to meet with students, lockers for graduate student use and vending machines. The McDougal Center is open days, evenings, and weekends.

5.1.3 Student Life Programs

The Center offers a variety of activities open to the Graduate and Professional community. These include weekly movies on the Really Big Screen, coffeehouse musical evenings, happy hours, poetry readings, students' research presentations, health and wellness workshops, teas with campus and community figures, and service opportunities such as blood drives. It hosts activities organized by student groups and departments, including cultural festivals, movies, lectures, receptions, and conferences. Activities are publicized in campus publications, in McDougal Notes calendar, on the website, and via email lists. Find out what’s going on at your Center today! Lisa Brandes, Director, Graduate Student Life, 123 HGS, 432-2583.

5.1.4 Graduate Career Services (GCS)

Graduate Career Services was established to guide and educate graduate students about academic and non-academic career opportunities and job search strategies. The office offers programs such as professional career development workshops, seminars, resume/CV reviews, individual counseling, on-campus interviews, dossier service and current job listings. Victoria Blodgett, 122 HGS, 432-7375 .

5.1.5 The Office of Teacher Preparation

The Office of Teaching Fellow Preparation and Development provides a wide variety of services and resources for graduate student teachers at Yale. In addition to coordinating teacher training and teaching resources in the graduate school, the office serves to facilitate departmental and faculty involvement in the development of Yale’s Teaching Fellows. Contact William Rando, Director, 432-7702, 123 HGS.

5.2 Life in the Department

The Department of Computer Science at Yale is a stimulating environment in which new ideas, experimental designs, and concrete artifacts are plentiful. In trying to shape the very nature of computer science, it is not enough to ask why things are, nor to ask how things will be — but rather, to ask how things should be now and in the future. How should computers be used in our society, and why? How should we design software, algorithms, new theories of computation? How should computer science be taught? What should the legacy of our efforts be?
Department Colloquium Series (in which distinguished researchers from other universities are invited on a monthly basis to speak to a general CS audience) Theory Seminar (hosting talks on all aspects of theoretical computer science) SPAM (the “Systems Personal Activity Meeting”, hosting talks on programming languages and systems, Vision Lunch (hosting talks on topics related to computer vision), CVC Round Table (open to any CS, EE, or Biomedical Engineering students, and focusing on computer vision, A.I., control theory, and biomedical engineering).

5.3 Life About Town

Yale is the focal point for much of the intellectual and cultural life of New Haven. Yale offers two symphony orchestras, a symphonic wind ensemble, a jazz ensemble, the Yale Repertory Theater, the Yale Art Gallery, the British Art Center, and more than a thousand informal concerts, recitals, and theatrical productions each year. Many of these events are presented by undergraduate members of Yale College; others are presented by the Schools of Fine Art, Drama, and Music.

Beyond the campus is a small Yankee town of 124,000. Birthplace of the cotton gin, the modern telephone exchange, and pizza, New Haven dates back to 1638. In the midst of a busy urban center, several areas of the city still retain the atmosphere of earlier days. Several clubs in the area feature jazz and rock bands. Late-night coffee houses near campus allow you to sit for hours over a cup of the best espresso south of Boston. Nearby is a 24-hour bookstore, a haven for fantasy and alternative literature enthusiasts. There are many movie theaters in the area, several featuring art films and retrospective shows.

Indeed, New Haven has a rich cultural life independent of that provided by the University. There is an excellent resident theater company, the Long Wharf Theatre, which produces plays from the standard repertoire and one or two new works each season. The historic Shubert Theater and the Palace present a wide selection of musical theater and drama. New Haven also has its own professional symphony orchestra, chamber ensembles, and a small ballet company. The town is also host of the widely acclaimed International Festival of Arts and Ideas. Every June, world-class theater, film, and dance productions, art and photography exhibits, panel discussions and poetry readings, and many musical events turn the city into a cultural and intellectual Mecca.

New Haven boasts a wide variety of culinary establishments, from the mundane to the exotic. Available at just about any hour is the “sub” sandwich and pizza, but a variety of other fare is also available at restaurants within walking distance of the central campus: Italian, Chinese, Mexican, Japanese, Thai, Indian, Cuban, and “natural".

For outdoor and sports enthusiasts, New Haven boasts professional hockey and baseball teams, the Connecticut Tennis Center (host of the annual Pilot Pen Tennis Tournament), and over 800 acres of beautiful trails and fields at nearby East and West Rock Parks for jogging and biking enjoyment. Yale’s famous Payne Whitney Gymnasium is open to students at no charge during the academic year and for a nominal fee in the summer. Students also have the opportunity to participate in numerous intramural sports activities during the year as well as individual sports activities such as golf, tennis, and figure skating. Sailing, rowing, and canoeing are also available at Yale facilities in nearby towns.

And of course New Haven, Connecticut is part of New England, and is thus in proximity to all of New England’s great resources; from its quaint towns, beautiful beaches and seaports to its mountain peaks and lakes for hiking, swimming, skiing, and mountaineering. It is also easy to reach the big city experience: New Haven is only 75 miles from New York and 100 miles from Boston, and both are connected by frequent and convenient train service.

6. Graduate Admissions and Financial Aid

6.1 Admissions Procedures

Students are admitted for entrance in the Fall term only. An applicant should have strong preparation in mathematics, engineering, or science. He or she should be competent in programming but needs no computer science beyond the basic level. The Graduate Record Examination Aptitude Test and some pertinent Advanced Achievement Tests are required (GRE General and Subject).

Application for admission in the Fall of 2010 should begin in the Fall of 2009. Forms may be obtained from:

http://www.yale.edu/graduateschool/admissions

Contact Information for the Graduate School is:

Graduate School Admissions
Yale University
117 Hall of Graduate Studies
320 York Street
New Haven, Connecticut 06511

Telephone: 203.432.2771

Applications to the Graduate School is an online process only.

Note that the Graduate School does not accept faxed copies of letters of recommendations, transcripts or other supplemental material.

Prospective students can obtain further Information by sending email to
graduate.admissions@yale.edu

The deadline for completed applications, including all letters of recommendation and test scores, is December 15, 2009.

Applicants will be notified of action concerning admission as soon as the decision has been made, generally between March 15 and April 1. Those who are undergraduates at the time of admission must present evidence of having satisfactorily completed the Bachelor’s degree or its equivalent in order to register. Those who are in graduate school must present transcripts giving evidence of satisfactory completion of the current year’s work prior to registration.

There is a non-refundable application fee of $90. Applicants from countries under exchange restrictions should seek the help of their state banks or of friends already in the United States for payment of this fee.

Applicants should arrange to take the GRE’s no later than October testing.The results of later testing are usually not available before admissions decisions are made. Remember that ETS will report scores only by mail and only at the written request of the student. Address inquiries to:

GRE-ETS
P.O. Box 6000
Princeton, NJ 08541-7670
609-771-7650
www.gre.org

Except by prearrangement with the Dean’s office, foreign applicants whose native language is not English must present evidence of proficiency in English by satisfactorily completing the Test of English as a Foreign Language, administered in foreign countries by the Educational Testing Service. TOEFL scores must be received by December 15th. Address inquiries to:

TOEFL/TSE Services - ETS GRE-ETS
P.O. Box 6000
Princeton, NJ 08541-7670
609-771-7650
www.toefl.org

6.2 Financial Aid Policy

The Department tries to find financial support for every student who needs it, for at least the first four years of study. During the first year, support is usually provided by a University Fellowship.

After the first year, students often receive research assistantships in their field of specialization or other forms of support. These may also be supplemented by teaching fellowships. The standard teaching fellowship in this department is at the level of a Teaching Fellow 2 and requires approximately 10 hours of work per week. Advanced students are sometimes supported through a combination of a University Fellowship and a teaching fellowship.

Only in exceptional cases is financial aid available after the fourth year. However, the lack of support is mitigated by the fact that a nominal “Continuous Registration Fee” (currently $680.00 per term) replaces the tuition requirement after the fourth year. (See the Graduate School “Programs and Policies” book for more information on the tuition policy.)

Applicants seeking financial aid must complete the forms included in the application packet sent out by the Graduate School.

7. Graduate Courses

Prerequisites that are part of the core of the undergraduate major are not listed. If you are not sure that your background is adequate, please speak to the instructor.

CPSC 521a Compilers and Interpreters. Zhong Shao
(Not taught in 2009-2010)
Compiler organization and implementation: lexical analysis, formal syntax specification, parsing techniques, execution environment, storage management, code generation and optimization, procedure linkage, and address binding. The effect of language-design decisions on compiler construction.

CPSC 522b Operating Systems. Bryan Ford
MW 1:00-2:15
The design and implementation of operating systems. Topics include synchronization, deadlock, process management, storage management, file systems, security, protection, and networking.

CPSC 524b Parallel Programming Techniques. Andrew Sherman
TTH 2:30-3:45
Practical introduction to high performance parallel computing, emphasizing techniques suitable for scientific and engineering applications. Aspects of processor and machine architecture relevant to parallel computing. Parallel programming paradigms: vector processing, multithreading, and message-passing. Selected algorithmic patterns for parallel scientific/engineering computations. Performance measurement, tuning, and debugging of parallel programs. Parallel file systems and I/O. Programming exercises may be completed in any programming language widely-used for scientific/engineering applications. (Not taught every year.)

CPSC 525b Theory of Distributed Systems. James Aspnes
MWF 11:35-12:25
Models of asynchronous distributed computing systems. Fundamental concepts of concurrency and synchronization, reliability, topological and geometric constraints, time and space complexity, and distributed algorithms. (Taught in alternate years.)

CPSC 527a Object-oriented Programming. Michael Fischer
TTH 1:00-2:15
Object-oriented programming as a means to efficient, reliable, modular, reusable code. Use of classes, derivation, templates, name-hiding, exceptions, polymorphic functions, and other features of C++. (Not taught every year).

CPSC528b Language-Based Security.
(Not taught in 2009-2010)
Basic design and implementation of language-based approaches for increasing the security and reliability of systems software. Topics include proof-carrying code; certifying compilation; typed assembly languages; runtime checking and monitoring; high-confidence embedded systems and drivers; and language support for verification of safety and liveness properties.

CPSC 530a Formal Semantics. Zhong Shao
Introduction to formal approaches to programming language design and implementation. Topics include the lambda-calculus, type theory, denotational semantics, type-directed compilation, higher-order modules, and application of formal methods to systems software and Internet programming. (Not taught every year).

CPSC 531a Computer Music – Algorithmic and Heuristic Composition
(Not taught in 2009-2010)
Study of the theoretical and practical fundamentals of computer-generated music, with a focus on high-level representations of music, algorithmic and heuristic composition, and programming languages for computer music generation. Theoretical concepts are supplemented with pragmatic issues expressed in a high-level programming language. Prerequisites: ability to read music; CPSC 202a and 223b.

CPSC 532a Computer Music – Sound Representation and Synthesis
MW 2:30-3:45 Paul Hudak
Study of the theoretical and practical fundamentals of computer-generated music, with a focus on low-level sound representation, acoustics and sound synthesis, scales and tuning systems, and programming languages for computer music generation. Theoretical concepts are supplemented with pragmatic issues expressed in a high-level programming language. (Taught in alternate years)
Prerequisites: Ability to read music. After CPSC 202a and 223b.

CPSC 533a Computer Networks. Yang Richard Yang
MW 2:30-3:45
An introduction to the design, implementation, analysis, and evaluation of computer networks and their protocols. Topics include layered network architectures, applications, transport, congestion, routing, data link protocols, local area networks, performance analysis, multimedia networking, network security, and network management. Emphasis on protocols used in the Internet. (Taught in alternate years.)

CPSC 534b Mobile Computing and Wireless Networking.
(Not taught in 2009-2010)
An introduction to the principles of mobile computing and its enabling technologies. Topics include principles of mobile computing; wireless systems; information management; location-independent/dependent computing models; disconnected and weakly connected operation models; human-computer interactions; mobile applications and services; security; power management; and sensor networks. (Taught in alternate years.)

CPSC 535b Internet-scale Applications. Yang Richard Yang
TTH 1:00-2:15
An introduction to the design and implementation of Internet-scale applications and services. Topics include: service-oriented software design; cloud computing paradigms; infrastructure scalability and reliability; adaptive, open clients; protocol specification; performance modeling; debugging and diagnosis; and deployment and licensing. (Not taught every year.)

CPSC 536a Networked Embedded Systems and Sensor Networks.
TTH 11:35-12:50 Andreas Savvides
Introduction to the fundamental concepts of networked embedded systems and wireless sensor networks, presenting a cross-disciplinary approach to the design and implementation of smart wireless embedded systems. Topics include embedded systems programming concepts; low-power and power-aware design; radio technologies; communication protocols for ubiquitous computing systems; and mathematical foundations of sensor behavior. Laboratory work includes programming assignments on low-power wireless devices. (Open to seniors in Computer Science or Electrical Engineering only.)

CPSC 537a Introduction to Databases. Avi Silberschatz
TTh 2:30-3:45
An introduction to database systems. Data modeling. The relational model and the SQL query language. Relational database design, integrity constraints, functional dependencies, and normal forms. Object-oriented databases. Database data structures: files, B-trees, hash indexes.

CPSC538b Database System Implementation and Architectures.
MW 2:30-3:45 Daniel Abadi
A study of systems programming techniques, with a focus on database systems. Half the course is spent studying the design of a traditional DBMS, supplemented by a hands-on exercise where students build various components (e.g., a catalog-manager, a buffer-manager, and a query execution engine) of a DBMS prototype. The other half is spent on non-traditional architectures (parallel databases, data warehouses, stream databases, Web databases).

CPSC 540b Numerical Computation I. Vladimir Rokhlin
TTH 1:00-2:15
Algorithms for numerical problems in the physical, biological, and social sciences: solution of linear and nonlinear systems of equations, interpolation and approximation of functions, numerical differentiation and integration, optimization.

CPSC 545b Introduction to Data Mining. Vladimir Rokhlin
TTH 1:00-2:15
A study of algorithms and systems that allow computers to find patterns and regularities in databases, to perform prediction and forecasting, and to improve their performance generally through interaction with data.

CPSC 555a/ECON 563a Economics and Computation
(Not taught in 2009-2010)
A mathematically rigorous investigation of the interplay of economic theory and CS with an emphasis on the relationship of incentive-compatibility and algorithmic efficiency. Particular attention will be paid to the formulation and solution of mechanism-design problems that are relevant to data networking and Internet-based commerce. (Not taught every year).

CPSC 561b Foundations of Cryptography.
(not taught in 2009-2020)
Foundations of modern cryptography and their application to computer and network security. Topics include randomized models of computation, indistinguishability, computationally hard problems, one-way and trapdoor functions, pseudorandom generators, zero-knowledge, secure computation, and probabilistic proofs.

CPSC 562a Graphs and Networks.
(Not taught in 2009-2010)
A mathematical examination of graphs and their applications in the sciences. Families of graphs include social networks, small-world graphs, Internet graphs, planar graphs, well-shaped meshes, power-law graphs, and classic random graphs. Phenomena include connectivity, clustering, communication, ranking, and iterative processes.

CPSC 563b Introduction to Machine Learning.
(Not taught in 2009-2010)
Paradigms and algorithms for learning classification rules and more complex behaviors from examples and other kinds of data. Topics may include version spaces, decision trees, artificial neural networks, Bayesian networks, instance-based learning, genetic algorithms, reinforcement learning, inductive logic programming, the MDL principle, the PAC model, VC dimension, sample bounds, boosting, support vector machines, queries, grammatical inference, and transductive and inductive inference.

CPSC 565a/MATH 511a Topics in Algorithms
(Not taught in 2009-2010)
Introduction to the fundamental tools used in approximation algorithms: linear, convex, and semi-definite programming; dynamic programming; and geometric tools. Recent progress in the design of approximation algorithms for graph problems, combinatorial problems, and other NP-hard optimization problems. Results on the hardness of approximation based on probabilistically checkable proofs. (Taught in alternate years).

CPSC 567a Cryptography and Computer Security Michael Fischer
MW 2:30-3:45
A survey of such private and public key cryptographic techniques as DES, RSA, and zero-knowledge proofs, and their application to problems of maintaining privacy and security in computer networks. Focus on technology, with consideration of such societal issues as balancing individual privacy concerns against the needs of law enforcement, vulnerability of societal institutions to electronic attack, export regulations and international competitiveness, and development of secure information systems.

CPSC 568a Computational Complexity. Joan Feigenbaum
TTh 2:30-3:45
Introduction to the theory of computational complexity. Basic complexity classes, including Polynomial Time, Nondeterministic Polynomial Time, Probabilistic Polynomial Time, Polynomial Space, Logarithmic Space, and Nondeterministic Logarithmic Space. The roles of reductions, completeness, randomness, and interaction in the formal study of computation.

CPSC 569b Randomized Algorithms.
(Not taught in 2009-2010)
Beginning with an introduction to tools from probability theory including some inequalities like Chernoff bounds, the course will cover randomized algorithms from several areas: graph algorithms, algorithms in algebra, approximate counting, probabilistically checkable proofs, and matrix algorithms. (Taught in alternative years.)

CPSC 570a Artificial Intelligence. Brian Scassellati
MWF 10:30 – 11:20 AKW 200
An introduction to artificial intelligence research, focusing on reasoning and perception. Topics include knowledge representation, predicate calculus, temporal reasoning, vision, robotics, planning, and learning.

CPSC 573b Intelligent Robotics. Brian Scassellati
MWF 10:30-11:20
An introduction to the construction of intelligent, autonomous systems. Sensory-motor coordination and task-based perception. Implementation techniques for behavior selection and arbitration, including behavior-based design, evolutionary design, dynamical systems, and hybrid deliverative-reactive systems. Situated learned and adaptive behavior.

CPSC 575b Computational Vision and Biological Perception.
MW 1:00-2:15 Steven Zucker
An overview of computational vision with a biological emphasis. Suitable as an introduction to biological perception for computer science and engineering students, as well as an introduction to computational vision for mathematics, psychology, and physiology students.

CPSC 577a Neural Networks for Computing . Willard Miranker
TTh 11:35 – 12:50
Artificial neural networks as a computational paradigm studied with application to problems in associative memory, learning, pattern recognition, perception, robotics, and other areas. Development of models for the dynamics of neurons and methods such as learning for
designing neural networks. Concepts, designs, and methods compared and tested in software simulation. Brain and consciousness studies are optional topics.

CPSC 578b Computer Graphics. Julie Dorsey
TTH 2:30-3:45
An introduction to the basic concepts of two- and three-dimensional computer graphics. Topics include affine and projective transformations, clipping and windowing, visual perception, scene modeling and animation, algorithms for visible surface determination, reflection models, illumination algorithms, and color theory. Assumes solid C or C++ programming skills and a basic knowledge of calculus and linear algebra.

CPSC 579a Advanced Topics in Computer Graphics. Holly Rushmeier
MW 1:00-2:15
An in-depth study of advanced algorithms and systems for rendering, modeling, and animation in computer graphics. Topics vary and may include reflectance modeling, global illumination, subdivision surfaces, NURBS, physically-based fluids systems, and character animation. (Not taught every year).

CPSC 662a/AMTH561a Spectral Graph Theory. Daniel Spielman
WF 2:30-3:45
An applied approach to Spectral Graph Theory. The combinatorial meaning of the eigenvalues and eigenvectors of matrices associated with graphs. Applications to optimization, numerical linear algebra, error-correcting codes, and testing graph isomorphism. (Not taught every year.)

CPSC 671a Advanced Artificial Intelligence. Drew McDermott
MW 1:00-2:15
Automated Planning, the problem of finding, for some sort of agent acting in some sort of environment, structures of actions and other commitments to achieve some goal and/or optimize some objective function while possibly avoiding violating constraints. Topics include representations for classical planning; complexity of classical planning; state-space planning; plan-space planning; planning-graph techniques; propositional satisfiability techniques; constraint satisfaction techniques; heuristics in planning; space applications; and planning for manufacturability analysis. (Not taught every year).

CPSC 690a or b Independent Project By arrangement with Faculty
Individual research for students in the PhD program. Requires a faculty supervisor and the permission of the director of graduate studies.

CPSC 691a or b Independent Project By arrangement with Faculty
Continuation of CPSC 690b or a.

CPSC 692a or b Independent Project By arrangement with Faculty
Individual research for students in the MS program. Requires a faculty supervisor and the permission of the director of graduate studies.

CPSC752b Bioinformatics: Practical Application of Simulation and
Data Mining. Mark Gerstein MW 1:00-2:15
Bioinformatics encompasses the computational analysis of gene sequences, macromolecular structures and functional genomics data on a large scale. It represents a major practical application for modern techniques in data mining and simulation. Specific topics to be covered include sequence alignment, large-scale processing next-generation sequencing data, comparative genomics, phylogenetics, biological database design, geometric analysis of protein structure, molecular-dynamics simulation, biological networks, normalization of micro array data, mining of functional genomics data sets, and machine learning approaches for data integration.

CPSC 820a Directed Readings in Programming Languages and Systems By arrangement with Faculty

CPSC 840a Directed Readings in Numerical Analysis By arrangement with Faculty

CPSC 860a Directed Readings in Theory By arrangement with Faculty

CPSC 870a Directed Readings in Artificial Intelligence
By arrangement with Faculty

Related Courses in Other Departments

ENAS 530a Optimization Techniques
ENAS 912a Biomedical Image Processing and Analysis
ENAS 875a Introduction to VLSI Systems Design
ENAS 944a Digital Communication Systems
ENAS 563a Fault-Tolerant Computer Systems
ENAS 525a Optimization I.
PHIL 567a Mathematical Logic I
PHIL 568b Mathematical Logic II
STAT 541a Probability Theory
STAT 542b Theory of Statistics
STAT 551b Stochastic Processes
STAT 664B//ENAS954b Information Theory
STAT 665b Data Mining and Machine Learning


8. Personnel

8.1 Advanced Students

Richard Alimi
RESEARCH AREA: Network Management

Christopher Crick
RESEARCH AREA: Role and Intent from Agent Motion

Samuel Daitch
RESEARCH AREA: Algorithms for Numerical Analysis

Ramzi Dakdouk
RESEARCH AREA: Theory and Application of Extractable Functions

Jiang Du
RESEARCH AREA: Optimal Integration of Sampling Techniques in
Bioinformatics

Rodrigo Ferriero
RESEARCH AREA: Formal Reasoning about Relaxed Memory Models

Aaron Johnson
RESEARCH AREA: Theory of Onion Routing

Elizabeth Kim
RESEARCH AREA: Human-robot interaction for social skills therapy
In autism, and discourse

Hai Liu
RESEARCH AREA: Functional Reactive Programming

Jianye Lu
RESEARCH AREA: Studies in Texture Generation of Weathered
Appearance from Captured Data

Lev Reyzin
RESEARCH AREA: Computational Learning Theory

Felipe Saint-Jean
RESEARCH AREA: Private Web Search

Jeffrey Sarnat
RESEARCH AREA: The Proof Theory of the Metatheory of Deductive
Systems

Nikhil Srivastava
RESEARCH AREA: Graph Algorithms by Electrical and Spectral
Methods

Alexander Vaynberg
RESEARCH AREA: Abstraction Methods for Static Software Verification

Bing Wang
RESEARCH AREA: Analysis and Synthesis of Natural Shapes

Chen Xu
RESEARCH AREA: Modeling Large Structures: Geometry and Appearance

Songhua Xu
RESEARCH AREA: Information Retrieval Biomedical Informatics

Yitong Yin
RESEARCH AREA: Complexity of Data Structures, Distributed Algorithms

8.2 Recent Graduates

Pavel Dimitrov, Research Specialist, Exxon Mobil Upstream
Thesis: Three Principles for Plant Geometry: How Vein Pattern
Formation in Leaves Informs Plant Growth, 2008

Xinyu Feng, Assistant Professor, Toyota Technological Institute
Thesis: An Open Framework for Certified System Software, 2008

Kevin Gold, Assistant Professor, Wellesley College
Thesis: Using Sentence Context and Implicit Contrast to Learn Sensor-Grounded Meanings for Relational and Deictic Words: 2008

Liwen Huang, Sr. Technical Staff, Oracle Corporation
Thesis: Functional Reactive Control of Humanoid Robots, 2008

Hong Jiang, Software Engineer, Google
Thesis: Distributed Systems of Simple Interacting Agents, 2008

Edo Liberty, Post-Doc Fellow, Yale University
Thesis: Accelerated Dense Random Projections, 2009

Andrew McCreight, Research Associate, Portland State University
Thesis: The Mechanized Verification of Garbage Collector
Implementations, 2008

Pradipta Mitra, Software Engineer, Google
Thesis: Clustering Algorithms for Random and Pseudo-random
Structures, 2008

Adam Poswolsky, Sr, Associate, Princeton Consultants
Thesis: Functional Programming with Logical Frameworks, 2008

Frederick Shic, Post-Doc Fellow, Yale Child Study Center
Thesis: Computational Methods for the Eye-Tracking Analysis:
Applications to Autism, 2008

Peishen Qi, Associate, JP Morgan
Thesis: Semantic Tuple Space Coordination for the Semantic Web
With Applications in Life Science, 2008

Hao Wang, Software Engineer, Google
Thesis: Efficient and Robust Traffic Engineering in a Dynamic
Environment, 2009

Yinghua Wu, Strategist, Morgan Stanley
Thesis: Fast Construction Algorithms for Overlay Networks, 2009

Haiyong Xie, Professor, University of Science & Technology, China
Thesis: Explicit Communications for Cooperative Internet Traffic
Control, 2009

Yuk-Lap Yip, Post-doc, Yale University
Thesis: Computational Reconstruction of Biological Networks, 2009

9. Graduate School Calendar

Schedule of Academic Dates and Deadlines 2009–2010

Fall Term 2009

Aug. 24 New student orientation week begins
Aug. 26 SPEAK Test for new international students in
Ph.D. programs
Aug. 27 Matriculation ceremony
Aug. 28 Fall-term Online Course Selection (OCS)
Begins
SPEAK Alternative Test for new International students
In Ph.D. programs
Sept 1 Registration for returning students begins
Orientation for all new Teaching Fellows
Sept. 2 Fall-term classes begin, 8:20 a.m.
Sept. 4 Final day to pick up registration materials from
Academic departments.
Sept. 7 Labor Day. Administrative office closed.
Sept 11 Final day to apply for a fall-term personal
leave of absence
The entire fall-term tuition charge or continuous
registration fee (CRF) will be canceled for
students who withdraw from the Graduate School
on or before this date or who are granted a leave
of absence effective on or before this date.
Sept. 16 Fall-term Online Course Selection (OCS) ends.
Final day for registration. A fee of $25 is
assessed for course schedules accepted after
this date
Sep.25 One-half of the fall-term full-tuition charge will be
canceled for students who withdraw from the
Graduate School on or before this date or who
are granted a medical leave of absence effective on
or before this date. The CRF is not prorated
Oct. 1 Final date for the faculty to submit grades to
replace grades of Temporary Incomplete (TI)
awarded during the previous academic year
Due date for dissertations to be considered by
the degree committees for award of the Ph.D.
in December
Final day to file petitions for degrees to be
awarded in December
Oct. 23 Midterm
One-quarter of the fall-term full-tuition charge
will be canceled for students who withdraw from
the Graduate School on or before this date or
who are granted a medical leave of absence
effective on or before this date. The CRF is
not prorated
Teaching appointments will not appear on the
transcripts of students who withdraw from the
assignment on or before this date
Oct. 30 Final day to change enrollment in a fall-term
course from credit to audit or from audit to credit
Final day to withdraw from a fall-term course
Nov. 2 Readers’ reports are due for dissertations to be
considered by the degree committees for
award of the Ph.D. in December
Nov. 6 Departmental recommendations are due for
candidates for December degrees
Final day to withdraw a degree petition for
degrees to be awarded in December
Nov. 12 SPEAK Test for international students in Ph.D.
Programs
Nov. 20 Fall recess begins, 5:20 p.m.
Nov. 30 Classes resume, 8:20 a.m.
Dec. 11 Classes end, 5:20 p.m.
Dec. 19 Fall term ends; winter recess begins

Spring Term 2010

Jan. 6 Final grades for fall-term courses due
Jan. 7 SPEAK Alternative Test for new international
students in Ph.D. programs
Jan. 11 Registration and spring ID validation begins
Spring-term classes begin, 8:20 a.m.
Jan. 15 Friday classes do not meet. Monday classes
meet instead
Jan. 18 Martin Luther King, Jr. Day. Administrative
offices closed. Classes do not meet
Jan. 20 Final day to apply for a spring-term personal
leave of absence
The entire spring-term tuition charge or CRF
will be canceled for students who withdraw
from the Graduate School on or before this
date or who are granted a leave of absence
effective on or before this date
Jan 22 Registration and spring ID validation end. Spring-
term Online Course Selection (OCS) ends. Final
day for registration. A fee of $25 is assessed for
forms accepted after this date
Feb. 5 One-half of the spring-term full-tuition charges
will be canceled for students who withdraw
from the Graduate School on or before this date
or who are granted a medical leave of absence
effective on or before this date. The CRF is not
prorated
Mar. 5 Midterm
Spring recess begins, 5:20 p.m.
One-quarter of the spring-term full-tuition charge
will be canceled for students who withdraw from
the Graduate School on or before this date or who
are granted a medical leave of absence effective on
or before this date. The CRF is not prorated
Teaching appointments will not appear on the
transcripts of students who withdraw from the
assignment on or before this date
Mar. 15 Due date for dissertations to be considered by
the Degree Committees for award of the Ph.D.
in May
Final day to file petitions for degrees to be
awarded in May
Mar. 22 Classes resume, 8:20 a.m.
Mar. 29 Final day to change enrollment in a spring-term
course from credit to audit or from audit to credit
Final day to withdraw from a spring-term course
Apr. 2 Good Friday. Administrative offices closed
Apr. 12 Readers’ reports are due for dissertations to be
considered by the degree committees for award
of the Ph.D. in May
Apr. 15 SPEAK Test for international students in Ph.D.
Programs
Apr. 21 Departmental recommendations are due for
candidates for May degrees
Apr. 23 Final day to withdraw a degree petition for degrees
to be awarded in May
Apr. 26 Monday classes do not meet. Friday classes meet
instead
April 30 Final day to submit Dissertation Progress Reports
And petitions for extended registration.
May 3 Classes end, 5:20 p.m.
May 11 Spring term ends
May 14 Final grades for spring-term courses are due for
candidates for terminal M.A. and M.S. degrees
to be awarded at Commencement
May 23 Graduate School Convocation
May 24 University Commencement
Jun. 1 Final grades for spring-term courses and full-
year courses are due
Jun. 4 SPEAK Alternative Test for new international
students in Ph.D. programs

Inquiries concerning the contents of this handbook may be referred to:

Director of Graduate Studies
Department of Computer Science
Yale University
P.O. Box 208285
New Haven, CT 06520-8285

email: gradinfo@cs.yale.edu
Phone: 203.432.1283

Last Revised: August 2009